You’ve been initiated into the baffling world of chocolate emulsions.
In mixing together the chocolate and the two liquids, you create an emulsion. An emulsion can have one of two configurations- the fat complex can envelope the water complex, or vice versa. Which of these happens will depend on many factors, including the proportion of chocolate to liquid. If you have large amounts of chocolate and only a little liquid, as is likely the case here, the fat camplex will do the enveloping. This kind of emulsion is inherently unstable. The fat and water complexes will appear to combine under agitation, but they will separate out once the agitation stops.
In many recipes, that would be really bad news, but probably not in this one. The proportions of the ingredients might not have even allowed this to happen. And even if you managed to create a nice, smooth fat-in-water emulsion (which you’d want in most other applications), that emulsion would have reversed when you mixed the whipped cream in (because the whipped cream is itself a water-in-fat emulsion). The most you could do in this recipe is integrate the emulsion as well as possible right before mixing in the rest of the stuff. Vigorous mixing is indeed called for, and a whisk would do a much better job of this than would a spoon.
In mousses that use whipped cream, it’s very important not to over whip the cream; the texture will be grainy otherwise. And the cream has to be last thing mixed in, because the fat in the other ingredients will begin to set up as soon as cold cream hits it, The cream has to get folded in very quickly and efficiently so that the mix homogenizes before the fat fully sets, then you mess with it as little as possible from that point on. any unnecessary mixing or manipulation after the fat sets will break down the aerated structure.
I’ve learned not to assume that published recipes (even ones from famous chefs) are workable. I’ve witnessed first-hand the half-assed way that many of these recipes are born.